Job ID = 6454691 SRX = SRX2520640 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:10 prefetch.2.10.7: 1) Downloading 'SRR5206759'... 2020-06-21T09:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:36:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:36:32 prefetch.2.10.7: 'SRR5206759' is valid 2020-06-21T09:36:32 prefetch.2.10.7: 1) 'SRR5206759' was downloaded successfully Read 14386095 spots for SRR5206759/SRR5206759.sra Written 14386095 spots for SRR5206759/SRR5206759.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:04 14386095 reads; of these: 14386095 (100.00%) were unpaired; of these: 346641 (2.41%) aligned 0 times 10921217 (75.92%) aligned exactly 1 time 3118237 (21.68%) aligned >1 times 97.59% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2097687 / 14039454 = 0.1494 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:44:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:36: 1000000 INFO @ Sun, 21 Jun 2020 18:44:42: 2000000 INFO @ Sun, 21 Jun 2020 18:44:48: 3000000 INFO @ Sun, 21 Jun 2020 18:44:54: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:45:00: 5000000 INFO @ Sun, 21 Jun 2020 18:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:45:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:07: 6000000 INFO @ Sun, 21 Jun 2020 18:45:08: 1000000 INFO @ Sun, 21 Jun 2020 18:45:15: 7000000 INFO @ Sun, 21 Jun 2020 18:45:16: 2000000 INFO @ Sun, 21 Jun 2020 18:45:22: 8000000 INFO @ Sun, 21 Jun 2020 18:45:24: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:45:30: 9000000 INFO @ Sun, 21 Jun 2020 18:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:45:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:33: 4000000 INFO @ Sun, 21 Jun 2020 18:45:38: 10000000 INFO @ Sun, 21 Jun 2020 18:45:39: 1000000 INFO @ Sun, 21 Jun 2020 18:45:41: 5000000 INFO @ Sun, 21 Jun 2020 18:45:46: 11000000 INFO @ Sun, 21 Jun 2020 18:45:47: 2000000 INFO @ Sun, 21 Jun 2020 18:45:49: 6000000 INFO @ Sun, 21 Jun 2020 18:45:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:45:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:45:53: #1 total tags in treatment: 11941767 INFO @ Sun, 21 Jun 2020 18:45:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:45:54: #1 tags after filtering in treatment: 11941683 INFO @ Sun, 21 Jun 2020 18:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:55: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 18:45:55: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:55: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:45:55: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 18:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:55: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 18:45:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:45:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:55: 3000000 INFO @ Sun, 21 Jun 2020 18:45:58: 7000000 INFO @ Sun, 21 Jun 2020 18:46:04: 4000000 INFO @ Sun, 21 Jun 2020 18:46:06: 8000000 INFO @ Sun, 21 Jun 2020 18:46:12: 5000000 INFO @ Sun, 21 Jun 2020 18:46:14: 9000000 INFO @ Sun, 21 Jun 2020 18:46:20: 6000000 INFO @ Sun, 21 Jun 2020 18:46:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:23: 10000000 INFO @ Sun, 21 Jun 2020 18:46:29: 7000000 INFO @ Sun, 21 Jun 2020 18:46:32: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.05_summits.bed INFO @ Sun, 21 Jun 2020 18:46:33: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:37: 8000000 INFO @ Sun, 21 Jun 2020 18:46:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:46:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:46:40: #1 total tags in treatment: 11941767 INFO @ Sun, 21 Jun 2020 18:46:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:46:40: #1 tags after filtering in treatment: 11941683 INFO @ Sun, 21 Jun 2020 18:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:41: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 18:46:41: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:41: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:46:41: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 18:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10_model.r WARNING @ Sun, 21 Jun 2020 18:46:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:41: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 18:46:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:46:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:45: 9000000 INFO @ Sun, 21 Jun 2020 18:46:53: 10000000 INFO @ Sun, 21 Jun 2020 18:47:00: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:07: #1 total tags in treatment: 11941767 INFO @ Sun, 21 Jun 2020 18:47:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:47:08: #1 tags after filtering in treatment: 11941683 INFO @ Sun, 21 Jun 2020 18:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:09: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 18:47:09: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:09: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:47:09: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 18:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20_model.r WARNING @ Sun, 21 Jun 2020 18:47:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:09: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 18:47:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:47:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.10_summits.bed INFO @ Sun, 21 Jun 2020 18:47:18: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520640/SRX2520640.20_summits.bed INFO @ Sun, 21 Jun 2020 18:47:47: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 4 millis CompletedMACS2peakCalling